ArticleGigaScience2022
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Machine learning and single-cell analysis uncover distinctive characteristics of CD300LG within the TNBC immune microenvironment: experimental validation.Clinical and experimental medicine · 2025Article
- Constitutional Epimutations: From Rare Events Toward Major Cancer Risk Factors?JCO precision oncology · 2025Review
- ConstitutionalHuman mutation · 2024Review
- Prenatal BRCA1 epimutations contribute significantly to triple-negative breast cancer development.Genome medicine · 2023Article
- Homologous Recombination Deficiency Across Subtypes of Primary Breast Cancer.JCO precision oncology · 2023Article
- epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data.GigaScience · 2022Article
- Constitutional BRCA1 Methylation and Risk of Incident Triple-Negative Breast Cancer and High-grade Serous Ovarian Cancer.JAMA oncology · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5-8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new area for translational research, detection of low-level mosaic epigenetic events requires highly sensitive and robust methodology for methylation analysis. We here present epialleleR, a computational framework for sensitive detection, quantification, and visualization of mosaic epimutations in methylation sequencing data. Analyzing simulated and real data sets, we provide in-depth assessments of epialleleR performance and show that linkage to epihaplotype data is necessary to detect low-level methylation events. The epialleleR is freely available at https://github.com/BBCG/epialleleR and https://bioconductor.org/packages/epialleleR/ as an open-source R/Bioconductor package.
Indexed as
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What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.